"Pokémon," while considered for kids, is a series enjoyed by people of every age whether they play the main series, spin-offs, "GO," or just watch the anime. It can be silly and funny but also dark and mysterious. From the creation of the World of Pokémon to Pokédex entries, the fandom is full of theories and lore.
Creation of the world
In the beginning, the Pokémon Arceus created Dialga and Palkia, the Pokémon of time and space. While Giratina was banished to the Distortion World the Lake Guardians were also brought into existence. Thus, the universe was born and Arceus went to sleep.
The legendary Pokémon, Groudon and Kyogre, natural enemies, clashed and formed land and seas with Rayquaza to come from the skies to quell their fighting. Regigigas then formed the continents and created Regirock, Regice, and Registeal, before being sealed away. Mew were abundant and eventually formed into other Pokemon until they went nearly extinct.
Two universes
The release of "Pokémon X" and "Pokemon Y" gave way to the introduction of mega evolution, a temporary evolution that surpassed the final evolution. During the remakes of "Ruby and Sapphire," "Omega Ruby," and "Alpha Sapphire," it was revealed that there are two different universes that were created; the world with mega evolution and the one without.
This gives us two timelines to the creation of the universe.
Paralyzed world
Time gears are stolen by the criminal Pokémon of the future, Grovyle, resulting in the freezing of time in those areas. The future is one where time is also frozen and desolate. This is presumably caused by Grovyle’s actions. Dusknoir and his Sableye come from the future to capture him and halt his plans.
The members of Wigglytuff’s guild are happy to be of help. Once they are ready to return to the future Dusknoir takes the hero and their partner with him to be disposed of. After aiding each other in the escape, the heroes learn the truth from Grovyle, though have trouble swallowing it. But together they return from the future to collect the time gears and place them in the Temporal Tower to prevent its ruin and the desolate future.
Dusknoir doesn’t make it easy, returning to stop them with the help of Primal Dialga. It is then revealed that not only is the hero Pokémon Groyvle’s partner from the future, but they are truly a human and if the tower is saved and the future changed, they will all disappear from existence.
Team Plasma
In "Black and White" the villainous Team Plasma is going around giving speeches, trying to convince people that the relationship between humans and their Pokémon is wrong and abusive toward the Pokémon. Pokémon should be free and wild, not captured in PokeBalls. This would sound nice if it wasn’t that the leader, Ghetsis, wanted to be the only one with Pokémon. For the beginning of his plan, he took in an orphan, N, who could talk to Pokémon.
Kept in captivity with a cushy life, N only spoke with Pokémon who had been hurt and abused. This gave him the belief that all humans treated Pokémon badly. He was just being used for Ghetsis’ plan to awake Unova’s legendary dragons.
Aether Foundation
In "Sun and Moon" Aether Foundation is a group meant to rehabilitate Pokémon but has dark secrets. While not all employees know what’s going on, the founder, Lusimine, not only funds Team Skull but cryogenically freezes Pokémon. Obsessed with the Ultra Beasts she has also worked to create Pokémon herself with the help of scientist Faba. Type: Full was supposed to be able to fight the Ultra Beasts; however, became uncontrollable and were changed to Type: Null and scheduled to be frozen.